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<body lang=ZH-CN link=blue vlink=purple style='tab-interval:21.0pt'>

<div class=WordSection1 style='layout-grid:15.6pt'>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>分析模块，输入<span class=GramE>转录组</span></span><span lang=EN-US
style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:
1.0pt'>BAM</span><span style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-font-kerning:1.0pt'>格式的比对结果文件（由分析模块“</span><span lang=EN-US
style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:
1.0pt'>HISAT2</span><span style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-font-kerning:1.0pt'>”生成），以及</span><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>GTF</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>格式的基因注释信息文件，计算</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>reads</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>在基因上的覆盖度。基因覆盖<span class=GramE>度分析</span>是样品中所有基因的</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'> 5</span><span class=GramE><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>’</span></span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>到</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'> 3</span><span class=GramE><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>’</span></span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>区域上序列覆盖情况的综合展现，用于评估测序实验结果的均<span class=GramE>一</span>性（或是偏向性）。</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><b
style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>输入：</span></b><b
style='mso-bidi-font-weight:normal'><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></b></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>1</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>、</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>bam</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>格式的比对结果文件，由分析模块“</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>HISAT2</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>”生成。</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>2</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>、基因模型文件，即</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>GTF</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>格式的注释信息文件。</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>关于</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>GTF</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>格式的基因注释信息文件，参考链接：（</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>http://asia.ensembl.org/info/website/upload/gff.html</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>）。</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><b
style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>输出：</span></b><b
style='mso-bidi-font-weight:normal'><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></b></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>1</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>、基因覆盖<span
class=GramE>度分析</span>作图结果。</span><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>示例：</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
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src="geneBody_coverage.files/image003.jpg" v:shapes="图片_x0020_1"><![endif]></span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
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<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>注：图中横坐标为单个基因的碱基长度占总碱基长度的百分比，</span><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>0</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>表示基因的</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'> 5</span><span
class=GramE><span style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-font-kerning:1.0pt'>’</span></span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>端，</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>100 </span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>表示基因的</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'> 3</span><span class=GramE><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>’</span></span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>端；纵坐标为比对到所有基因的横轴位置上相应区间内的序列条数的总和。图中体现了所有基因覆盖情况的叠加结果，曲线中每个点的纵坐标表示所有基因在该相对比例位置上所有序列的数量；曲线反映了测序所得序列是否在基因上均匀分布。如果在靠近左端有明显的峰值，说明测序结果有明显的</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>5</span><span class=GramE><span style='mso-bidi-font-size:
12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>’</span></span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>偏向性。如果在靠近右端有明显的峰值，说明测序结果有明显的</span><span lang=EN-US style='mso-bidi-font-size:
12.0pt;mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>3</span><span
class=GramE><span style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-font-kerning:1.0pt'>’</span></span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>偏向性。</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>2</span><span style='mso-bidi-font-size:12.0pt;
font-family:"微软雅黑","sans-serif";mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-font-kerning:1.0pt'>、覆盖度计算结果文件。</span><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>分析模块引用了</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'>RSeQC-2.5</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>软件包（</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'>http://rseqc.sourceforge.net/</span><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>）。</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
style='mso-bidi-font-size:12.0pt;font-family:"微软雅黑","sans-serif";mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-font-kerning:
1.0pt'>相关文献如下所示：</span><span lang=EN-US style='mso-bidi-font-size:12.0pt;
mso-fareast-font-family:微软雅黑;mso-font-kerning:1.0pt'><o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>Wang, L., Wang, S., &amp; Li, W. (2012). <span
class=SpellE>RSeQC</span>: quality control of RNA-<span class=SpellE>seq</span>
experiments. Bioinformatics (Oxford, England), 28(16), 2184�C2185.
http://doi.org/10.1093/bioinformatics/bts356<o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'>Wang, L., <span class=SpellE>Nie</span>, J., <span
class=SpellE>Sicotte</span>, H., Li, Y., <span class=SpellE>Eckel-Passow</span>,
J. E., <span class=SpellE>Dasari</span>, S., et al. (2016). <span class=GramE>Measure
transcript integrity using RNA-<span class=SpellE>seq</span> data.</span> BMC
Bioinformatics, 17(1), 1�C16. http://doi.org/10.1186/s12859-016-0922-z<o:p></o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal style='text-indent:20.0pt;mso-char-indent-count:2.0'><span
lang=EN-US style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:微软雅黑;
mso-font-kerning:1.0pt'><o:p>&nbsp;</o:p></span></p>

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